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Check the growth rate (called GrowthRate in pokemon.txt) for each species. They should be the same for ones that evolve into each other. Beldum/Metang/Metagross have a Slow growth rate.
To quantify: Pokémon have a set amount of XP at any one time, the growth rate determines how much XP to a level, so if you have a Pokémon evolve into Pokémon with a slower growth rate, it'll "lose" some levels, since each level requires more XP.